SMTL ID : 3v57.1 (1 other biounit)

Crystal Structure of the B-phycoerythrin from the red algae Porphyridium Cruentum at pH8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-3-3-mer

Ligands

15 x PEB: PHYCOERYTHROBILIN(Non-covalent)(Covalent)

PEB.1: 25 residues within 4Å: Chain A: F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, L.92, W.108, G.109, Y.117, L.120, L.122, P.123, A.126, Y.127 Chain F: S.57, I.67, T.75, N.76, M.79 31 PLIP interactions: 27 interactions with chain A, 4 interactions with chain F Hydrophobic interactions: A:A.72, A:K.78, A:K.81, A:K.81, A:H.88, A:Y.89, A:L.92, A:Y.117, A:L.120, A:L.122, A:A.126, A:Y.127, A:Y.127, F:I.67, F:M.79 Hydrogen bonds: A:K.78, A:R.84, A:D.85, A:H.88, A:Y.127, F:S.57, F:T.75 Water bridges: A:K.81, A:K.81, A:K.81, A:R.84, A:H.88 Salt bridges: A:K.78, A:K.81, A:R.84 pi-Cation interactions: A:H.88 PEB.2: 13 residues within 4Å: Chain A: K.43, L.44, N.47, A.50, V.51, E.54, R.137, L.138, C.139, R.142, D.143, M.144, F.152 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:K.43, A:A.50, A:V.51, A:R.137, A:F.152 Hydrogen bonds: A:K.43, A:N.47, A:R.142, A:R.142 Water bridges: A:K.43, A:D.143, A:D.143 Salt bridges: A:R.137, A:R.142 pi-Cation interactions: A:R.137, A:R.142 PEB.5: 17 residues within 4Å: Chain B: M.59, N.72, C.73, R.77, R.78, A.81, C.82, D.85, I.88, R.108, L.113, Y.117, L.120, V.122, P.123, S.126, S.127 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.78, B:A.81, B:I.88, B:I.88, B:L.120, B:V.122 Hydrogen bonds: B:D.85 Water bridges: B:R.78, B:R.84 Salt bridges: B:R.77, B:R.78 PEB.6: 17 residues within 4Å: Chain A: L.24, E.25, Q.28 Chain B: A.32, N.35, K.36, L.38, D.39, A.40, I.142, T.143, N.144, F.153, A.154, A.155, G.156, C.158 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:N.35, B:K.36, B:L.38, B:L.38, B:N.144, B:F.153, B:F.153, B:A.154, A:L.24 Hydrogen bonds: B:N.35, B:D.39, B:A.154, B:G.156, A:Q.28 Water bridges: B:N.35, B:N.35, B:N.35, B:K.36 PEB.7: 17 residues within 4Å: Chain B: N.47, C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, Q.137, A.140, F.141, A.146, T.147, E.148, R.149 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:D.54, B:I.133, B:I.133, B:A.136, B:Q.137, B:A.140, B:A.146 Hydrogen bonds: B:D.54, B:Q.137, B:T.147, B:E.148 Water bridges: B:E.62, B:R.129, B:R.129, B:A.136, B:E.148, B:E.148 Salt bridges: B:R.129 PEB.9: 25 residues within 4Å: Chain B: S.57, I.67, T.75, N.76, M.79 Chain C: F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, L.92, W.108, G.109, Y.117, L.120, L.122, P.123, A.126, Y.127 31 PLIP interactions: 5 interactions with chain B, 26 interactions with chain C Hydrophobic interactions: B:I.67, B:M.79, C:A.72, C:K.78, C:K.81, C:K.81, C:H.88, C:Y.89, C:L.92, C:Y.117, C:L.120, C:L.122, C:A.126, C:Y.127, C:Y.127 Hydrogen bonds: B:S.57, B:T.75, C:K.78, C:R.84, C:D.85, C:H.88, C:Y.127 Water bridges: B:S.57, C:K.81, C:K.81, C:R.84, C:H.88 Salt bridges: C:K.78, C:K.81, C:R.84 pi-Cation interactions: C:H.88 PEB.10: 13 residues within 4Å: Chain C: K.43, L.44, N.47, A.50, V.51, E.54, R.137, L.138, C.139, R.142, D.143, M.144, F.152 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:K.43, C:A.50, C:V.51, C:R.137, C:F.152 Hydrogen bonds: C:K.43, C:N.47, C:R.142, C:R.142 Water bridges: C:K.43, C:D.143, C:D.143 Salt bridges: C:R.137, C:R.142 pi-Cation interactions: C:R.137, C:R.142 PEB.13: 17 residues within 4Å: Chain D: M.59, N.72, C.73, R.77, R.78, A.81, C.82, D.85, I.88, R.108, L.113, Y.117, L.120, V.122, P.123, S.126, S.127 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:R.78, D:A.81, D:I.88, D:I.88, D:L.120, D:V.122 Hydrogen bonds: D:D.85 Water bridges: D:R.78, D:R.84 Salt bridges: D:R.77, D:R.78 PEB.14: 17 residues within 4Å: Chain C: L.24, E.25, Q.28 Chain D: A.32, N.35, K.36, L.38, D.39, A.40, I.142, T.143, N.144, F.153, A.154, A.155, G.156, C.158 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:N.35, D:K.36, D:L.38, D:L.38, D:N.144, D:F.153, D:F.153, D:A.154, C:L.24 Hydrogen bonds: D:N.35, D:D.39, D:A.154, D:G.156, C:Q.28 Water bridges: D:N.35, D:N.35, D:N.35, D:K.36 PEB.15: 17 residues within 4Å: Chain D: N.47, C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, Q.137, A.140, F.141, A.146, T.147, E.148, R.149 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:D.54, D:I.133, D:I.133, D:A.136, D:Q.137, D:A.140, D:A.146 Hydrogen bonds: D:D.54, D:Q.137, D:T.147, D:E.148 Water bridges: D:E.62, D:R.129, D:R.129, D:A.136, D:E.148, D:E.148 Salt bridges: D:R.129 PEB.17: 25 residues within 4Å: Chain D: S.57, I.67, T.75, N.76, M.79 Chain E: F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, L.92, W.108, G.109, Y.117, L.120, L.122, P.123, A.126, Y.127 31 PLIP interactions: 26 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:A.72, E:K.78, E:K.81, E:K.81, E:H.88, E:Y.89, E:L.92, E:Y.117, E:L.120, E:L.122, E:A.126, E:Y.127, E:Y.127, D:I.67, D:M.79 Hydrogen bonds: E:K.78, E:R.84, E:D.85, E:H.88, E:Y.127, D:S.57, D:T.75 Water bridges: E:K.81, E:K.81, E:R.84, E:H.88, D:S.57 Salt bridges: E:K.78, E:K.81, E:R.84 pi-Cation interactions: E:H.88 PEB.18: 13 residues within 4Å: Chain E: K.43, L.44, N.47, A.50, V.51, E.54, R.137, L.138, C.139, R.142, D.143, M.144, F.152 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:K.43, E:A.50, E:V.51, E:R.137, E:F.152 Hydrogen bonds: E:K.43, E:N.47, E:R.142, E:R.142 Water bridges: E:K.43, E:D.143, E:D.143 Salt bridges: E:R.137, E:R.142 pi-Cation interactions: E:R.137, E:R.142 PEB.21: 17 residues within 4Å: Chain F: M.59, N.72, C.73, R.77, R.78, A.81, C.82, D.85, I.88, R.108, L.113, Y.117, L.120, V.122, P.123, S.126, S.127 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:R.78, F:A.81, F:I.88, F:I.88, F:L.120, F:V.122 Hydrogen bonds: F:D.85 Water bridges: F:R.78, F:R.84 Salt bridges: F:R.77, F:R.78 PEB.22: 17 residues within 4Å: Chain E: L.24, E.25, Q.28 Chain F: A.32, N.35, K.36, L.38, D.39, A.40, I.142, T.143, N.144, F.153, A.154, A.155, G.156, C.158 18 PLIP interactions: 16 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:N.35, F:K.36, F:L.38, F:L.38, F:N.144, F:F.153, F:F.153, F:A.154, E:L.24 Hydrogen bonds: F:N.35, F:D.39, F:A.154, F:G.156, E:Q.28 Water bridges: F:N.35, F:N.35, F:N.35, F:K.36 PEB.23: 17 residues within 4Å: Chain F: N.47, C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, Q.137, A.140, F.141, A.146, T.147, E.148, R.149 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:D.54, F:I.133, F:I.133, F:A.136, F:Q.137, F:A.140, F:A.146 Hydrogen bonds: F:D.54, F:Q.137, F:T.147, F:E.148 Water bridges: F:E.62, F:R.129, F:R.129, F:A.136, F:E.148, F:E.148 Salt bridges: F:R.129

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: L.122, P.123, T.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.124, A:T.124 Water bridges: A:S.125 SO4.4: 1 residues within 4Å: Chain A: P.141 No protein-ligand interaction detected (PLIP) SO4.8: 3 residues within 4Å: Chain B: M.1, D.107, R.108 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.1, B:M.1, B:D.107 Salt bridges: B:R.108 SO4.11: 3 residues within 4Å: Chain C: L.122, P.123, T.124 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.124, C:T.124 Water bridges: C:S.125 SO4.12: 1 residues within 4Å: Chain C: P.141 No protein-ligand interaction detected (PLIP) SO4.16: 3 residues within 4Å: Chain D: M.1, D.107, R.108 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:M.1, D:M.1, D:D.107 Salt bridges: D:R.108 SO4.19: 3 residues within 4Å: Chain E: L.122, P.123, T.124 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.124, E:T.124 Water bridges: E:S.125 SO4.20: 1 residues within 4Å: Chain E: P.141 No protein-ligand interaction detected (PLIP) SO4.24: 3 residues within 4Å: Chain F: M.1, D.107, R.108 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:M.1, F:M.1, F:D.107 Salt bridges: F:R.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Camara-Artigas, A. et al., pH-dependent structural conformations of B-phycoerythrin from Porphyridium cruentum. Febs J. (2012)

Release Date

2012-10-03

Peptides

Phycoerythrin alpha subunit: ACE
Phycoerythrin beta subunit: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Phycoerythrin alpha subunit

Phycoerythrin beta subunit

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